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Merge pull request #441 from aodn/2.5.27
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2.5.27
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@ggalibert
ggalibert authored Jun 15, 2017
2 parents 9ac27d5 + 988d15e commit 6f5bbc9
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Showing 15 changed files with 151 additions and 122 deletions.
3 changes: 1 addition & 2 deletions AutomaticQC/CTDSurfaceSoakQC.m
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Expand Up @@ -130,7 +130,6 @@

% transform flags to the appropriate output shape
sizeData = size(data);
sizeData(sizeData == lenData) = 1;
flags = repmat(flags, sizeData);
flags = repmat(flags, [1 sizeData(2:end)]);
end
end
5 changes: 2 additions & 3 deletions AutomaticQC/imosInOutWaterQC.m
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Expand Up @@ -157,6 +157,5 @@

% transform flags to the appropriate output shape
sizeData = size(data);
sizeData(sizeData == lenData) = 1;
flags = repmat(flags, sizeData);
end
flags = repmat(flags, [1 sizeData(2:end)]);
end
4 changes: 2 additions & 2 deletions AutomaticQC/imosRateOfChangeQC.m
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Expand Up @@ -8,8 +8,8 @@
% ascribed to the current data point of the set.
%
% Action: PARAMETER values are flagged if
% |Vi � Vi-1| + |Vi � Vi+1| > 2�(threshold)
% where Vi is the current value of the parameter, Vi�1
% |Vi - Vi-1| + |Vi - Vi+1| > 2*(threshold)
% where Vi is the current value of the parameter, Vi-1
% is the previous and Vi+1 the next one. If
% the one parameter is missing, the relative part of
% the formula is omitted and the comparison term
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2 changes: 1 addition & 1 deletion AutomaticQC/imosTiltVelocitySetQC.m
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Expand Up @@ -186,7 +186,7 @@

if isempty(firstTiltThreshold)
% couldn't find this instrument so quit the test
disp(['Info: imosTiltVelositySetQC could not be performed on ' sample_data.toolbox_input_file ...
disp(['Warning: imosTiltVelositySetQC could not be performed on ' sample_data.toolbox_input_file ...
' instrument = "' instrument '" => Fill imosTiltVelositySetQC.txt with relevant make/model information if you wish to run this test on this dataset.']);
return;
end
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6 changes: 3 additions & 3 deletions Graph/checkMooringPlannedDepths.m
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Expand Up @@ -291,18 +291,18 @@ function checkMooringPlannedDepths(sample_data, isQC, saveToFile, exportDir)
%comparison
%This could be done better, with more finesse - could allow zooming in
%before going straight to the time period selection. For now, this will do.
hMsgbox = msgbox('Select the time period for comparison using the mouse', 'Time Period Selection', 'help', 'modal');
hMsgbox = msgbox('Select (drag & drop) a time period on the top graph for comparison, preferably at the start of deployment, when the mooring is standing vertical', 'Time Period Selection', 'help', 'modal');
uiwait(hMsgbox);

%select the area to use for comparison
[x,y] = select_points(hAxPress);
[x, ~] = select_points(hAxPress);

%now plot the difference from planned depth data:
iGood = timeVar >= x(1) & timeVar <= x(2);
dataVar(~iGood) = NaN;
minDep = min(dataVar,[],2);

hLineVar2 = scatter(hAxDepthDiff, ...
scatter(hAxDepthDiff, ...
metaDepth, ...
minDep - metaDepth, ...
15, ...
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5 changes: 3 additions & 2 deletions Graph/checkMooringPresDiffs.m
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Expand Up @@ -15,7 +15,8 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
% exportDir - string containing the destination folder to where the
% plot is saved on disk.
%
% Author: Rebecca Cowley <[email protected]>
% Author: Rebecca Cowley <[email protected]>
% Contributor: Guillaume Galibert <[email protected]>
%

%
Expand Down Expand Up @@ -165,7 +166,7 @@ function checkMooringPresDiffs(sample_data, iSampleMenu, isQC, saveToFile, expor
set(get(hAxPressDiff, 'XLabel'), 'String', 'Time');
set(get(hAxPressDiff, 'YLabel'), 'String', ['Pressure differences (' varUnit ')'], 'Interpreter', 'none');
set(get(hAxPressDiff, 'Title'), 'String', ...
['Pressure differences in ' varUnit ' (minus respective median over 1st quarter) between ' instrumentDesc{iCurrSam} ' (in black above) and nearest neighbours'] , 'Interpreter', 'none');
['Pressure differences in ' varUnit ' (minus respective median over 1st quarter) between ' instrumentDesc{iCurrSam} ' (in black above) and 4 (max) nearest neighbours'] , 'Interpreter', 'none');
set(hAxPressDiff, 'XTick', (xMin:(xMax-xMin)/4:xMax));
set(hAxPressDiff, 'XLim', [xMin, xMax]);
hold(hAxPressDiff, 'on');
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4 changes: 2 additions & 2 deletions IMOS/imosParameters.txt
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Expand Up @@ -72,8 +72,8 @@ HEIGHT_ABOVE_SENSOR, 1, height,
HL, 1, surface_upward_latent_heat_flux, W m-2, , , F, 999999.0, , , float
HS, 1, surface_upward_sensible_heat_flux, W m-2, , , F, 999999.0, , , float
ISO17, 1, depth_of_isosurface_of_sea_water_potential_temperature, m, down, sea surface, E, 999999.0, , , float
LATITUDE, 1, latitude, degrees_north, , WGS84 coordinate reference system, , 999999.0, -90.0, 90.0, double
LONGITUDE, 1, longitude, degrees_east, , WGS84 coordinate reference system, , 999999.0, -180.0, 180.0, double
LATITUDE, 1, latitude, degrees_north, , WGS84 geographic coordinate system, , 999999.0, -90.0, 90.0, double
LONGITUDE, 1, longitude, degrees_east, , WGS84 geographic coordinate system, , 999999.0, -180.0, 180.0, double
LW, 1, surface_downwelling_longwave_flux_in_air, W m-2, , , F, 999999.0, , , float
LW_NET, 1, surface_net_upward_longwave_flux, W m-2, , , F, 999999.0, , , float
MASS_NET, 1, upward_mass_flux_of_air, kg m-2 s-1, , , F, 999999.0, , , float
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38 changes: 23 additions & 15 deletions Parser/readParadoppBinary.m
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Expand Up @@ -191,20 +191,26 @@
isPairInconsistent = [xor(isPairInconsistent(1:end-1), isPairInconsistent(2:end)); false] & isPairInconsistent;
end

% sometimes, inconsistencies are due to the file simply being corrupted
% in this case we just remove the faulty Sync (also handles the case when
% the last section has been truncated so that we don't try to read it at all)
iSync(iSync) = isSizeConsistent;

iIds = [false; iSync(1:end-1)];
ids = data(iIds);
uniqIds = unique(sort(ids));

iSizes = [false; false; iSync(1:end-2)] | [false; false; false; iSync(1:end-3)];
sizesFromData = bytecast(data(iSizes), 'L', 'uint16', cpuEndianness)*2; % 1 word = 2 bytes

% when size info not available from sector we replace it with its expected value
for i=1:length(noSizeIds), sizesFromData(ids == noSizeIds(i)) = noSizeSize(i); end
% now we need to deal with any fault sync detection left alone
if any(~isSizeConsistent)
iSync(iSync) = [true; isSizeConsistent(1:end-1)];

% we also handle the case when the last section has been truncated so
% that we don't try to read it at all
if ~isSizeConsistent(end)
iSync(iSync) = [true(sum(iSync)-1, 1); false];
end

iIds = [false; iSync(1:end-1)];
ids = data(iIds);
uniqIds = unique(sort(ids));

iSizes = [false; false; iSync(1:end-2)] | [false; false; false; iSync(1:end-3)];
sizesFromData = bytecast(data(iSizes), 'L', 'uint16', cpuEndianness)*2; % 1 word = 2 bytes

% when size info not available from sector we replace it with its expected value
for i=1:length(noSizeIds), sizesFromData(ids == noSizeIds(i)) = noSizeSize(i); end
end
clear iIds iSizes sizesFromSync;

% now we can read data sectors by type
Expand Down Expand Up @@ -280,8 +286,10 @@
clear dataSection;
iBadChecksum = cs ~= vertcat(sect(:).Checksum);
if any(iBadChecksum)
% we don't want a keep a section with erroneous data in it
% we don't want to keep a record with erroneous data in it
sect(iBadChecksum) = [];

if isempty(sect), continue; end
end
clear cs iBadChecksum;

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1 change: 0 additions & 1 deletion Parser/readWQMraw.m
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Expand Up @@ -187,7 +187,6 @@
[name, comment] = getParamDetails(varlabel{k}, params);

data = wqmdata.(varlabel{k});
data(iBadTime) = [];

% some fields are not in IMOS uom - scale them so that they are
switch varlabel{k}
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49 changes: 34 additions & 15 deletions Parser/workhorseParse.m
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Expand Up @@ -130,13 +130,33 @@
cellStart + (numCells-1) * cellLength)';

% rearrange the sample data
time = datenum(...
[variable.y2kCentury*100 + variable.y2kYear,...
variable.y2kMonth,...
variable.y2kDay,...
variable.y2kHour,...
variable.y2kMinute,...
variable.y2kSecond + variable.y2kHundredth/100.0]);
instrument_firmware = strcat(num2str(fixed.cpuFirmwareVersion(1)), '.', num2str(fixed.cpuFirmwareRevision(1))); % we assume the first value is correct for the rest of the dataset
if str2double(instrument_firmware) > 8.35
time = datenum(...
[variable.y2kCentury*100 + variable.y2kYear,...
variable.y2kMonth,...
variable.y2kDay,...
variable.y2kHour,...
variable.y2kMinute,...
variable.y2kSecond + variable.y2kHundredth/100.0]);
else
% looks like before firmware 8.35 included, Y2K compliant RTC time
% was not implemented
century = 2000;
if variable.rtcYear(1) > 70
% first ADCP was built in the mid 1970s
% hopefully this firmware will no longer be used
% in 2070...
century = 1900;
end
time = datenum(...
[century + variable.rtcYear,...
variable.rtcMonth,...
variable.rtcDay,...
variable.rtcHour,...
variable.rtcMinute,...
variable.rtcSecond + variable.rtcHundredths/100.0]);
end

timePerPing = fixed.tppMinutes*60 + fixed.tppSeconds + fixed.tppHundredths/100;
timePerEnsemble = fixed.pingsPerEnsemble .* timePerPing;
Expand Down Expand Up @@ -252,16 +272,15 @@

end

sample_data.meta.instrument_model = [model ' Workhorse ADCP'];
sample_data.meta.instrument_serial_no = serial;
sample_data.meta.instrument_sample_interval = median(diff(time*24*3600));
sample_data.meta.instrument_average_interval = mode(timePerEnsemble);
sample_data.meta.instrument_firmware = ...
strcat(num2str(fixed.cpuFirmwareVersion(1)), '.', num2str(fixed.cpuFirmwareRevision(1))); % we assume the first value is correct for the rest of the dataset
sample_data.meta.instrument_model = [model ' Workhorse ADCP'];
sample_data.meta.instrument_serial_no = serial;
sample_data.meta.instrument_sample_interval = median(diff(time*24*3600));
sample_data.meta.instrument_average_interval = mode(timePerEnsemble);
sample_data.meta.instrument_firmware = instrument_firmware;
if all(isnan(fixed.beamAngle))
sample_data.meta.beam_angle = 20; % http://www.hydro-international.com/files/productsurvey_v_pdfdocument_19.pdf
sample_data.meta.beam_angle = 20; % http://www.hydro-international.com/files/productsurvey_v_pdfdocument_19.pdf
else
sample_data.meta.beam_angle = mode(fixed.beamAngle); % we set a static value for this variable to the most frequent value found
sample_data.meta.beam_angle = mode(fixed.beamAngle); % we set a static value for this variable to the most frequent value found
end

% add dimensions with their data mapped
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146 changes: 74 additions & 72 deletions Preprocessing/timeDriftPP.m
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Expand Up @@ -105,86 +105,88 @@
end
end

f = figure(...
'Name', 'Time start and end drift calculations in seconds',...
'Visible', 'off',...
'MenuBar' , 'none',...
'Resize', 'off',...
'WindowStyle', 'Modal',...
'NumberTitle', 'off');

cancelButton = uicontrol('Style', 'pushbutton', 'String', 'Cancel');
confirmButton = uicontrol('Style', 'pushbutton', 'String', 'Ok');

setCheckboxes = [];
startOffsetFields = [];
endOffsetFields = [];

for k = 1:nSample
if ~auto
f = figure(...
'Name', 'Time start and end drift calculations in seconds',...
'Visible', 'off',...
'MenuBar' , 'none',...
'Resize', 'off',...
'WindowStyle', 'Modal',...
'NumberTitle', 'off');

setCheckboxes(k) = uicontrol(...
'Style', 'checkbox',...
'String', descs{k},...
'Value', 1, ...
'UserData', k);
cancelButton = uicontrol('Style', 'pushbutton', 'String', 'Cancel');
confirmButton = uicontrol('Style', 'pushbutton', 'String', 'Ok');

startOffsetFields(k) = uicontrol(...
'Style', 'edit',...
'UserData', k, ...
'String', num2str(startOffsets(k)));
setCheckboxes = [];
startOffsetFields = [];
endOffsetFields = [];

endOffsetFields(k) = uicontrol(...
'Style', 'edit',...
'UserData', k, ...
'String', num2str(endOffsets(k)));
for k = 1:nSample

setCheckboxes(k) = uicontrol(...
'Style', 'checkbox',...
'String', descs{k},...
'Value', 1, ...
'UserData', k);

startOffsetFields(k) = uicontrol(...
'Style', 'edit',...
'UserData', k, ...
'String', num2str(startOffsets(k)));

endOffsetFields(k) = uicontrol(...
'Style', 'edit',...
'UserData', k, ...
'String', num2str(endOffsets(k)));

end

end

% set all widgets to normalized for positioning
set(f, 'Units', 'normalized');
set(cancelButton, 'Units', 'normalized');
set(confirmButton, 'Units', 'normalized');
set(setCheckboxes, 'Units', 'normalized');
set(startOffsetFields, 'Units', 'normalized');
set(endOffsetFields, 'Units', 'normalized');

set(f, 'Position', [0.2 0.35 0.6 0.0222 * (nSample + 1)]); % need to include 1 extra space for the row of buttons

rowHeight = 1 / (nSample + 1);

set(cancelButton, 'Position', [0.0 0.0 0.5 rowHeight]);
set(confirmButton, 'Position', [0.5 0.0 0.5 rowHeight]);

for k = 1:nSample
% set all widgets to normalized for positioning
set(f, 'Units', 'normalized');
set(cancelButton, 'Units', 'normalized');
set(confirmButton, 'Units', 'normalized');
set(setCheckboxes, 'Units', 'normalized');
set(startOffsetFields, 'Units', 'normalized');
set(endOffsetFields, 'Units', 'normalized');

set(f, 'Position', [0.2 0.35 0.6 0.0222 * (nSample + 1)]); % need to include 1 extra space for the row of buttons

rowHeight = 1 / (nSample + 1);

set(cancelButton, 'Position', [0.0 0.0 0.5 rowHeight]);
set(confirmButton, 'Position', [0.5 0.0 0.5 rowHeight]);

for k = 1:nSample

rowStart = 1.0 - k * rowHeight;

set(setCheckboxes (k), 'Position', [0.0 rowStart 0.6 rowHeight]);
set(startOffsetFields (k), 'Position', [0.6 rowStart 0.2 rowHeight]);
set(endOffsetFields (k), 'Position', [0.8 rowStart 0.2 rowHeight]);
end

% set back to pixels
set(f, 'Units', 'normalized');
set(cancelButton, 'Units', 'normalized');
set(confirmButton, 'Units', 'normalized');
set(setCheckboxes, 'Units', 'normalized');
set(startOffsetFields, 'Units', 'normalized');
set(endOffsetFields, 'Units', 'normalized');

rowStart = 1.0 - k * rowHeight;
% set widget callbacks
set(f, 'CloseRequestFcn', @cancelCallback);
set(f, 'WindowKeyPressFcn', @keyPressCallback);
set(setCheckboxes, 'Callback', @checkboxCallback);
set(startOffsetFields, 'Callback', @startoffsetFieldCallback);
set(endOffsetFields, 'Callback', @endoffsetFieldCallback);
set(cancelButton, 'Callback', @cancelCallback);
set(confirmButton, 'Callback', @confirmCallback);

set(setCheckboxes (k), 'Position', [0.0 rowStart 0.6 rowHeight]);
set(startOffsetFields (k), 'Position', [0.6 rowStart 0.2 rowHeight]);
set(endOffsetFields (k), 'Position', [0.8 rowStart 0.2 rowHeight]);
set(f, 'Visible', 'on');

uiwait(f);
end

% set back to pixels
set(f, 'Units', 'normalized');
set(cancelButton, 'Units', 'normalized');
set(confirmButton, 'Units', 'normalized');
set(setCheckboxes, 'Units', 'normalized');
set(startOffsetFields, 'Units', 'normalized');
set(endOffsetFields, 'Units', 'normalized');

% set widget callbacks
set(f, 'CloseRequestFcn', @cancelCallback);
set(f, 'WindowKeyPressFcn', @keyPressCallback);
set(setCheckboxes, 'Callback', @checkboxCallback);
set(startOffsetFields, 'Callback', @startoffsetFieldCallback);
set(endOffsetFields, 'Callback', @endoffsetFieldCallback);
set(cancelButton, 'Callback', @cancelCallback);
set(confirmButton, 'Callback', @confirmCallback);

set(f, 'Visible', 'on');

uiwait(f);

% calculate the drift and apply to the selected datasets
for k = 1:nSample

Expand Down
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